Aaron Alexis, the 34-year-old suspect who was killed by police during Monday’s shooting, received a security clearance more than five years ago when he was still in the Navy and kept it in his most recent job as a technology contractor at the Navy Yard.

Critics in Congress and elsewhere say his ability to keep his security clearance despite a history of misconduct, including while in uniform, shows serious flaws in the system.

Hagel, addressing reporters for the first time since the shooting in which 13 people were killed including Alexis, said his deputy, Ashton Carter, would undertake two reviews – an examination of physical security and access procedures at all Defense Department installations worldwide.

Carter’s review will look at the U.S. military’s practices and procedures for granting and renewing security clearances, including those held by contractors like Alexis.

“Obviously, when you go back in hindsight and look at all this there were some red flags – of course there were,” Hagel said.

“And should we have picked them up? Why didn’t we? How could we have? All those questions need to be answered.”

General Martin Dempsey, chairman of the Joint Chiefs of Staff, said it would have been hard to foresee Monday’s bloodshed. “I don’t know what the investigation will determine, but he committed murder. And I’m not sure that any particular question or lack of question on a security clearance would probably have revealed that.”

Dempsey was also hesitant to adopt the term “red flag.” “Until I understand the outcome of the investigation, I can’t render a judgment about whether it was a red flag or just something that flew beneath the radar.”

Alexis’ secret-level security clearance would have been valid for 10 years, without the need for a renewal that could have led to new disclosures about his conduct.

Hagel said the length of time clearances are valid would be one of the areas under examination.

“Obviously, the longer clearances go without review, there is some jeopardy to that. There’s no question about it,” he said.

Alexis’ initial background check was conducted as part of his service in the U.S. Navy Reserve from May 2007 to January 2011. He underwent a National Agency Check that was completed in August 2007 and he was determined eligible to handle “secret” material in March 2008, a U.S. defense official said.

That check for his security clearance was conducted after Alexis was arrested in Seattle in 2004 for shooting a construction worker’s car tires in an anger-fueled “blackout,” according to the Seattle Police Department.

The “secret” clearance was in effect during two other incidents.

In 2008, Alexis was cited for disorderly conduct in Georgia when he was kicked out of a club for damaging furnishings and cursing. Alexis was then arrested in 2010 in Texas for discharging a firearm in a case that was dropped after investigators determined his gun accidentally fired while it was being cleaned.

In 2011 Alexis received an honorable discharge from the Navy Reserve, even though the Navy had been pursuing a general discharge against him on a series of eight to 10 misconduct charges, ranging from traffic offenses to disorderly conduct, a military official said.

Private pre-employment background checks also apparently failed to properly flag Alexis as a security risk. The Experts Inc, an information technology company that hired Alexis to work on a project helping service the Navy Marine Corps intranet, said it had also enlisted a service to perform two background checks on him over the last year.

The checks revealed no issues other than one minor traffic violation, the company said.